Microfluidics commonly refers to the study, control, and manipulation of fluids within small, enclosed channels having a variety of geometries. Microfluidic devices have proven invaluable for analyzing trace biological and chemical samples because the performance characteristics of analytical separations scale favorably with reduced channel dimensions, and because the integration of sample processing steps with a separation on the same device or “microchip” can be readily achieved. An emerging subfield of microfluidics, referred to as “droplet-based” or “plug-based” microfluidics, involves the encapsulation of aqueous droplets within another immiscible fluid such as an oil. The droplets can be formed uniformly in terms of both size and frequency, and offer the potential to serve as ideal reaction vessels for extremely small samples, including individual biological cells. If an entirely aqueous system were used, the contents that are normally contained in a droplet would diffuse into the surrounding solution, rapidly lowering the concentration of the constituent being detected.
Currently, detection of the contents of droplets typically occurs by passing a droplet through an optical detector, which measures, for example, the fluorescence emitted by a molecule of interest. This detection strategy, and those like it, have severe limitations in that chemical separations are essentially precluded, and only natively fluorescent species or those that have been fluorescently labeled can be detected. As such, only a small number of species can be measured within each droplet. Furthermore, current approaches to transfer droplets from the immiscible fluid to an aqueous one for subsequent separation/analysis typically results in large sample losses and/or require painstaking manipulation of individual droplets using optical trapping techniques. Accordingly, a need exists for methods and apparatuses for rapidly and easily handling samples in droplet-based microfluidic analysis that enables alternative detection approaches, especially those that conserve the content of the droplets and that are compatible with analytical separations prior to detection.